How to Subset a Giotto Object?#

There are several ways to subset a Giotto object or visualize a subset of the data. Below are some subsetting examples.

Note

Figures may not be identical, because examples might have been updated, but the subsetting principles remain the same.

1. The Visium 10X Whole Brain#

spatDimPlot(visium_brain, cell_color = 'leiden_clus',
plot_alignment = 'horizontal', spat_point_size = 2)
Visium 10X Whole Brain Image

2. Show Only A Subset of Clusters#

spatDimPlot(visium_brain,
    cell_color = 'leiden_clus',  select_cell_groups = '4',
    plot_alignment = 'horizontal', spat_point_size = 2)
Show only a subset of clusters

3. Show Only A Subset of Clusters (excluding not selected cells)#

spatDimPlot(visium_brain,
    cell_color = 'leiden_clus',  select_cell_groups = '4', show_other_cells = F,
    plot_alignment = 'horizontal', spat_point_size = 2)
Excluding not selected cells

4. Create Spatial Plots#

These spatial plots have been grouped by the Leiden Clustering results

spatPlot(visium_brain,
    group_by = 'leiden_clus', group_by_subset = c(1:8),
    cell_color = 'leiden_clus', cow_n_col = 4,
    point_size = 1, axis_text = 6, axis_title = 6, legend_text = 6)
Leiden group 1 
spatPlot(visium_brain,
    group_by = 'leiden_clus', group_by_subset = c(9:16),
    cell_color = 'leiden_clus', cow_n_col = 4,
    point_size = 1, axis_text = 6, axis_title = 6, legend_text = 6)
Leiden group 2

5. Create Dimension Plots#

These dimension plots have been grouped by the HMRF results.

spatDimPlot(visium_brain, cell_color = 'HMRF_k12_b.1',
      plot_alignment = 'horizontal', spat_point_size = 2)
HMRF Whole Brain 
dimPlot(visium_brain,
    group_by = 'HMRF_k12_b.1', group_by_subset = c(1:6),
        cell_color = 'leiden_clus', cow_n_col = 3,
    point_size = 1, axis_text = 6, axis_title = 6, legend_text = 6)
HMRF Whole Brain by group 1 
dimPlot(visium_brain,
    group_by = 'HMRF_k12_b.1', group_by_subset = c(7:14),
        cell_color = 'leiden_clus', cow_n_col = 3,
        point_size = 1, axis_text = 6, axis_title = 6, legend_text = 6)
HMRF Whole Brain by group 2

6. Create A New Giotto Object By Subsetting Selected Clusters#

metadata = pDataDT(visium_brain)
subset_cell_IDs = metadata[leiden_clus %in% c(4, 5, 8, 13)]$cell_ID
visium_brain_small = subsetGiotto(visium_brain, cell_ids = subset_cell_IDs)

spatDimPlot(visium_brain_small,
     cell_color = 'leiden_clus',
     plot_alignment = 'horizontal', spat_point_size = 2.5)
Subsetting selected clusters 
spatDimPlot(visium_brain_small,
     cell_color = 'nr_genes', color_as_factor = F,
     plot_alignment = 'horizontal', spat_point_size = 2.5)
Subset brain nr

7. Create A New Giotto Object By Subsetting Spatial Coordinates/Locations#

DG_subset = subsetGiottoLocs(visium_brain,
             x_max = 6500, x_min = 3000,
             y_max = -2500, y_min = -5500)

spatDimPlot(DG_subset,
    cell_color = 'leiden_clus',
    plot_alignment = 'horizontal', spat_point_size = 4,
    save_param = list(save_name = '6_DG_loc_subset', base_height = 4))
Subset based on spatial coordinates/locations